Structural Biochemistry

Objectives

Available soon

General characterization

Code

7637

Credits

6.0

Responsible teacher

Maria João Lobo de Reis Madeira Crispim Romão

Hours

Weekly - 4

Total - Available soon

Teaching language

Português

Prerequisites

Available soon

Bibliography

  • Structural Biology, Practical NMR applications, Quincy Teng, Springer (2005)
  • H.J. Dyson, A.G. Palmer, “1.9 Introduction to Solution State NMR Spectroscopy”, Comprehensive Biophysics, 136-159, Edward H. Egelman, Eds, Elsevier (2012)
  • “Introduction to Protein Structure”   Branden, C.-I. & Tooze, J. Garland Pub. (1999)
  • “Crystallography made Crystal Clear- A Guide for users of Macromolecular Models” G. Rhodes, 2nd Ed., Academic Press: San Diego, London (2000)
  • Recent publications (articles and reviews) will be made available each year

Teaching method

Available soon

Evaluation method

Available soon

Subject matter

Part I

- Basic Concepts in NMR (review); 1D and 2D spectra (homo-and hetero-nuclear): applications to proteins

- Identification and assignment of signals in protein 2D spectra; secondary structural elements determination based on chemical shifts

- Backbone assignment of proteins using triple resonance experiments - methodology

- Determination of protein structures in solution; NMR constraints and methodology for structure calculations

- Relaxation and protein dynamics

- NOE effect and Saturation Transfer Difference experiments: application to protein - ligand interactions

- NH exchange and protein structural information.

Part II

- Introduction to protein crystallography; review

- Crystallization of proteins; Lattice, Symmetry and Space Groups

- X-ray sources and detectors; diffraction; reciprocal space

- Diffraction and Fourier transform; The Phase Problem and how to solve it.

- Model building and Refinement; Methods of Validation

- Molecular Electron Microscopy 

 

Practical Classes

NMR solution structure

- P1 : The NMR spectrometer ; 2D heteronuclear experiments.

- P2 : Resonance assignment using 3D spectra. Introduction to BMRB  - Biological Magnetic Resonance Data Bank.

- P3 : Solution structures determination using Cyana software - input data preparation,  output data (violations detection & iterative process) and validation results (online tools). NMR vs X-ray structures.

- P4 : Protein ligand interactions; titrations followed by HSQC and data obtained by STD (eg CBM11 )

- S : Case study Oral presentation and discussion

X-Ray Crystallography

- P1: databases, PDB revisited

- P2: Preparation and optimization of protein crystals (Q1)

- P3: The X-ray diffractometer and diffraction experiment. Processing and analysis of data.

- P4: Solving a structure by MR method (Q2)

- P5: Analysis of electron density and model building; Model quality and validation criteria. (Q3)

- S: Seminars – Case study : Oral presentation and discussion